Question: low coverage & BAF plots have three peaks
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gravatar for lait
19 months ago by
lait140
lait140 wrote:

our last sequencing run (WES, ILLUMINA) gave us low coverage for our samples (still we do not know why!). When I tried to produce the density for the b-allele frequency (calculated from the vcf files), the plots appeared to have three peaks instead of one. What could be the explanation for this? and could this help explain the low coverage we have?

ADD COMMENTlink written 19 months ago by lait140

Please share the figures.

ADD REPLYlink written 19 months ago by Kevin Blighe50k

here is a link to the figure.

ADD REPLYlink written 19 months ago by lait140

all others with three peaks are similar to this one.

ADD REPLYlink written 19 months ago by lait140

Can you provide some further context about what you are doing? For example, you mention that the coverage was "low" - how low is "low"? id you reduce QC filtering thresholds in response to that?

Also, are you following some tutorial or published work

ADD REPLYlink written 19 months ago by Kevin Blighe50k
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